Blender crashing during the execution of a script processeing moderatly to large graphs from graph_tool
After much messing around I found I was doing two things wrong. 

The first was I should have been importing graph tool with from graph_tool.all import graph_tool as gt instead of import graph_tool as gt.

The second problem I was having was not symlinking correctly. Instead of symlinking the whole site-packages I found that only symlinking what I actually needed worked.

I wrote the following bash script which will do all the necessary sym-linking given the name of the blender installation folder(this is so it will work for different versions of blender). You'll have to change the paths specifying where your conda installation is and what folder your blender installation directory is.

#pass it the blender installation directory. You will have to change $Blender_folder_directory to wherever you installed anaconda.
#Also make sure the anaconda environemnt is called blender
condaInstallation=/home/ben
Blender_folder_directory=/home/ben #which directory your blender installation folder is in.
name=$1
version=${name:8:4}

ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/graph_tool $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/scipy $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/cairo $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/matplotlib $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/dateutil $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/mpl_toolkits $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/gi $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages

ln $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/pyparsing.py $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/pyparsing-2.4.7.dist-info $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages

ln $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/cycler.py $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/cycler-0.10.0.dist-info $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages

ln $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/six.py $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/six-1.15.0.dist-info $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages


ln $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/kiwisolver.cpython-37m-x86_64-linux-gnu.so $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages
ln -s $condaInstallation/anaconda3/envs/blender/lib/python3.7/site-packages/kiwisolver-1.2.0.dist-info $Blender_folder_directory/$name/$version/python/lib/python3.7/site-packages